Understanding Metabolic Pathways

• Biochemistry explores the chemical processes within and relating to living organisms.
• It integrates organic chemistry, which studies carbon compounds, with biology.
• The field aims to explain the structure, function, and interactions of biological molecules.

Metabolic Pathways

• Metabolic pathways are a series of interconnected biochemical reactions.
• These reactions convert specific biomolecules into other related molecules.
• Each step in a pathway is catalyzed by a specific enzyme.
• Pathways can be linear, branched, or cyclic.
• Metabolic pathways are broadly classified into catabolic and anabolic processes.
• Catabolic pathways involve the breakdown of complex molecules into simpler ones, often releasing energy.
• Anabolic pathways use energy to synthesize complex molecules from simpler precursors.
• Glycolysis is a catabolic pathway that breaks down glucose into pyruvate.
• Gluconeogenesis is an anabolic pathway that synthesizes glucose from non-carbohydrate precursors.
• The citric acid cycle (Krebs cycle) oxidizes acetyl-CoA, producing energy carriers.
• Oxidative phosphorylation uses the energy from electron transport to produce ATP.
• Fatty acid synthesis and degradation are crucial metabolic pathways.
• Metabolic pathways are tightly regulated to maintain homeostasis.
• Regulation occurs through enzyme activity modulation and gene expression control.
• Feedback inhibition is a common regulatory mechanism.

Protein Synthesis

• Protein synthesis, also called translation, is the process of creating proteins from mRNA templates.
• It occurs in ribosomes, which are complex molecular machines.
• The process involves three main stages: initiation, elongation, and termination.
• Initiation starts with the binding of mRNA and the initiator tRNA to the ribosome.
• Elongation involves the addition of amino acids to the growing polypeptide chain.
• Termination occurs when a stop codon in the mRNA is encountered.
• tRNA molecules carry specific amino acids to the ribosome.
• Each tRNA has an anticodon that pairs with a specific codon on the mRNA.
• Aminoacyl-tRNA synthetases attach the correct amino acid to its corresponding tRNA.
• Peptide bonds are formed between adjacent amino acids.
• The ribosome moves along the mRNA in a 5' to 3' direction.
• Protein folding is essential for protein function.
• Chaperone proteins assist in proper protein folding.
• Post-translational modifications can alter protein structure and function.
• These modifications include phosphorylation, glycosylation, and ubiquitination.

Enzyme Function

• Enzymes are biological catalysts that accelerate biochemical reactions.
• They are typically proteins, but some RNAs can also act as enzymes (ribozymes).
• Enzymes lower the activation energy of a reaction, making it more likely to occur.
• Enzymes have a specific active site where substrates bind.
• The enzyme-substrate complex is formed through non-covalent interactions.
• Enzymes exhibit high specificity for their substrates.
• The "lock and key" and "induced fit" models describe enzyme-substrate interactions.
• Enzyme activity is affected by factors such as temperature, pH, and substrate concentration.
• Enzymes can be regulated by inhibitors and activators.
• Competitive inhibitors bind to the active site, preventing substrate binding.
• Non-competitive inhibitors bind to a different site, altering the enzyme's shape.
• Allosteric enzymes have multiple binding sites and exhibit cooperative binding.
• Cofactors and coenzymes are non-protein molecules that assist enzymes in catalysis.
• Vitamins are often precursors to coenzymes.
• Enzyme kinetics studies the rate of enzyme-catalyzed reactions.
• The Michaelis-Menten equation describes the relationship between reaction rate and substrate concentration.
• The Michaelis constant (Km) is the substrate concentration at which the reaction rate is half of its maximum value (Vmax).

Nucleic Acid Chemistry

• Nucleic acids are polymers of nucleotides.
• There are two main types of nucleic acids: DNA and RNA.
• DNA (deoxyribonucleic acid) stores genetic information.
• RNA (ribonucleic acid) plays various roles in gene expression.
• Nucleotides consist of a nitrogenous base, a pentose sugar, and a phosphate group.
• The nitrogenous bases in DNA are adenine (A), guanine (G), cytosine (C), and thymine (T).
• The nitrogenous bases in RNA are adenine (A), guanine (G), cytosine (C), and uracil (U).
• The pentose sugar in DNA is deoxyribose, while in RNA it is ribose.
• DNA is a double-stranded helix with complementary base pairing.
• Adenine pairs with thymine (A-T), and guanine pairs with cytosine (G-C).
• RNA is typically single-stranded, but it can form complex secondary structures.
• mRNA (messenger RNA) carries genetic information from DNA to ribosomes.
• tRNA (transfer RNA) carries amino acids to ribosomes during protein synthesis.
• rRNA (ribosomal RNA) is a component of ribosomes.
• DNA replication is the process of copying DNA.
• DNA polymerase is the enzyme that catalyzes DNA replication.
• Transcription is the process of synthesizing RNA from a DNA template.
• RNA polymerase is the enzyme that catalyzes transcription.
• The central dogma of molecular biology describes the flow of genetic information: DNA → RNA → Protein.
• Mutations are changes in the DNA sequence.
• Polymerase chain reaction (PCR) is a technique for amplifying specific DNA sequences.
• Restriction enzymes cut DNA at specific sequences.
• Nucleic acid hybridization is the process of base pairing between complementary DNA or RNA strands.

Cell Signaling

• Cell signaling is the process by which cells communicate with each other.
• It involves the transmission of signals from one cell to another.
• Signaling pathways control various cellular processes, including growth, differentiation, and apoptosis.
• There are several types of cell signaling: endocrine, paracrine, autocrine, and direct contact.
• Endocrine signaling involves hormones that travel through the bloodstream to distant target cells.
• Paracrine signaling involves local mediators that affect nearby cells.
• Autocrine signaling involves cells responding to signals they produce themselves.
• Direct contact signaling involves direct physical interaction between cells.
• Signal transduction is the process by which a cell converts one kind of signal into another.
• Receptors are proteins that bind to signaling molecules (ligands).
• Cell surface receptors bind to ligands that cannot cross the plasma membrane.
• Intracellular receptors bind to ligands that can cross the plasma membrane.
• G protein-coupled receptors (GPCRs) are a common type of cell surface receptor.
• Receptor tyrosine kinases (RTKs) are another type of cell surface receptor.
• Second messengers, such as cAMP and calcium ions, relay signals inside the cell.
• Kinases are enzymes that phosphorylate proteins, activating or inactivating them.
• Phosphatases are enzymes that remove phosphate groups from proteins.
• Signaling pathways are often regulated by feedback loops.
• Apoptosis is programmed cell death, a critical process for development and homeostasis.
• Dysregulation of cell signaling can lead to diseases, including cancer.